2FCC

Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with a DNA Substrate Containing Abasic Site

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.4	293	2 M (NH4)2SO4 and 0.1 M sodium citrate buffer (pH 6.4), VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 184.059	α = 90
b = 184.059	β = 90
c = 100.855	γ = 120

Symmetry
Space Group	P 64 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 4		2002-08-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X26C	0.9188	NSLS	X26C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.3	40	99.6	0.068	11.5	5.9		81403			21.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.34	99.2		0.393

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1VAS	2.3	39.85	81403	4032	96.1	0.249	0.249	0.274	RANDOM	41

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
2.36	0.6		2.36		-4.72

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	20.5
c_scangle_it	3.19
c_scbond_it	2.12
c_mcangle_it	1.95
c_mcbond_it	1.21
c_angle_deg	1.1
c_improper_angle_d	1.05
c_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2254
Nucleic Acid Atoms	1036
Solvent Atoms	183
Heterogen Atoms	22

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.